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MobleyLab / alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations
MIT License
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Problem with the Curve-Fitting-Method-based consistency inspector #34

Open julimox opened 9 years ago

julimox commented 9 years ago

As suggested I move my post from Pymbar to here.

I am running pymbar 3.0 with the alchemical_analysis without problems except for the " -c " flag.

On the provided sample input data it is running fine but if I want to use it on my dhdl files I get the following mistake:

Plotting the CFM figure... /opt/soft/anaconda-2.2.0/lib/python2.7/site-packages/matplotlib/axes/_base.py:2562: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=17.7338848684, right=17.7338848684 'left=%s, right=%s') % (left, right)) /opt/soft/anaconda-2.2.0/lib/python2.7/site-packages/matplotlib/axes/_base.py:2562: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=17.7624749232, right=17.7624749232 'left=%s, right=%s') % (left, right))

In case this is of interest: The dhdl-files were generated with Gromacs 5.0.4

My files are at

https://drive.google.com/folderview?id=0B2M9aqeJrxnYYTlsdU9jMnBQOGs&usp=sharing

Best regards, Julian

FEPanalysis commented 9 years ago

Julian,

The attached files are of 1.0 ps, i.e. 6 snapshots, each which is not long enough to see what, if any, the problem is. What I can tell right away is that the "-c" analysis does not crash. Should they be of more reasonable length, I will be more specific.

davidlmobley commented 9 years ago

Yes, please send the input files to reproduce the problem.

Thanks.

On Thu, Oct 22, 2015 at 12:46 PM, FEPanalysis notifications@github.com wrote:

Julian,

The attached files are of 1.0 ps, i.e. 6 snapshots, each which is not long enough to see what, if any, the problem is. What I can tell right away is that the "-c" analysis does not crash. Should they be of more reasonable length, I will be more specific.

— Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/34#issuecomment-150335672 .

David Mobley Associate Professor Department of Pharmaceutical Sciences Department of Chemistry 3134B Natural Sciences I University of California, Irvine Irvine, CA 92697 dmobley@uci.edu work (949) 824-6383 cell (949) 385-2436

julimox commented 9 years ago

I had cut the files more than I wanted to - sorry for that. The files updated to 100ps are now in the folder.

julimox commented 9 years ago

A kind reminder in case this issue is getting forgotten.

davidlmobley commented 9 years ago

Sorry about that. Pavel (@Fepanalysis) said he'll look at it next week. I thought he'd put that on GitHub but I see now it was only to me.

Thanks and sorry for the delay.

On Wed, Oct 28, 2015 at 4:39 AM, julianzachmann notifications@github.com wrote:

A kind reminder in case this issue is getting forgotten.

— Reply to this email directly or view it on GitHub https://github.com/MobleyLab/alchemical-analysis/issues/34#issuecomment-151811630 .

David Mobley dmobley@gmail.com 949-385-2436

FEPanalysis commented 9 years ago

Julian,

After a quick look the problem seems to be in bad overlap -- not the actual one (the consistency between TI and BAR suggests there is no real problem) but as it is understood by the CFM function which produces empty boxes. Seems to be a bug that needs to be fixed. Thanks for the warning and test data. I'll be spending more time with it next week.